The annotated variants are based on the following underlying tools and knowledge resources:
The report is generated with PCGR version dev, using the following key settings:
IMPORTANT NOTE: All SNV/InDel analyses below are considering the filtered callset only, n = 1665
The prioritization of SNV/InDels is here done according to a four-tiered structure, adopting the joint consensus recommendation by the ACMG (Li et al. 2017).
The table below permits filtering of the total SNV/InDel set by various criteria.
NOTE 1: The filtering applies to this table only, and not to the tier-specific tables below.
NOTE 2: Filtering on sequencing depth/allelic fraction depends on input specified by user (VCF INFO tags).
No variant-evidence item associations found.
No variant-evidence item associations found.
No variant-evidence item associations found.
No variant-evidence item associations found.
The following user-defined thresholds determine copy number aberrations shown here:
A total of 75 unfiltered aberration segments satisfied the above criteria.
A total of copy number segments satisfy the current filtering criteria.
A total of 0 proto-oncogenes are covered (i.e. transcript overlapping >= 50%) by genomic segments subject to amplifications.
A total of 0 tumor suppressor genes are covered (i.e. transcript overlapping >= 50%) by genomic segments subject to homozygous deletions.
A total of 0 aberrations are associated with clinical evidence items in the database for clinical interpretations of variants in cancer, CIViC, with the following number of evidence items:
No variant-evidence item associations found.
No variant-evidence item associations found.
No variant-evidence item associations found.
No variant-evidence item associations found.
No variant-evidence item associations found.
No variant-evidence item associations found.
Alexandrov, Ludmil B, Serena Nik-Zainal, David C Wedge, Samuel A J R Aparicio, Sam Behjati, Andrew V Biankin, Graham R Bignell, et al. 2013. “Signatures of Mutational Processes in Human Cancer.” Nature 500 (7463): 415–21.
Alexandrov, Ludmil B, Serena Nik-Zainal, David C Wedge, Peter J Campbell, and Michael R Stratton. 2013. “Deciphering Signatures of Mutational Processes Operative in Human Cancer.” Cell Rep. 3 (1): 246–59.
Cortes-Ciriano, Isidro, Sejoon Lee, Woong-Yang Park, Tae-Min Kim, and Peter J Park. 2017. “A Molecular Portrait of Microsatellite Instability Across Multiple Cancers.” Nat. Commun. 8: 15180.
Dong, Fei, Phani K Davineni, Brooke E Howitt, and Andrew H Beck. 2016. “A BRCA1/2 Mutational Signature and Survival in Ovarian High-Grade Serous Carcinoma.” Cancer Epidemiol. Biomarkers Prev. 25 (11): 1511–6.
Kim, Jaegil, Kent W Mouw, Paz Polak, Lior Z Braunstein, Atanas Kamburov, Grace Tiao, David J Kwiatkowski, et al. 2016. “Somatic ERCC2 Mutations Are Associated with a Distinct Genomic Signature in Urothelial Tumors.” Nat. Genet. 48 (6): 600–606.
Li, Marilyn M, Michael Datto, Eric J Duncavage, Shashikant Kulkarni, Neal I Lindeman, Somak Roy, Apostolia M Tsimberidou, et al. 2017. “Standards and Guidelines for the Interpretation and Reporting of Sequence Variants in Cancer: A Joint Consensus Recommendation of the Association for Molecular Pathology, American Society of Clinical Oncology, and College of American Pathologists.” J. Mol. Diagn. 19 (1): 4–23.
Rosenthal, Rachel, Nicholas McGranahan, Javier Herrero, Barry S Taylor, and Charles Swanton. 2016. “DeconstructSigs: Delineating Mutational Processes in Single Tumors Distinguishes DNA Repair Deficiencies and Patterns of Carcinoma Evolution.” Genome Biol. 17 (1): 31.
Secrier, Maria, Xiaodun Li, Nadeera de Silva, Matthew D Eldridge, Gianmarco Contino, Jan Bornschein, Shona MacRae, et al. 2016. “Mutational Signatures in Esophageal Adenocarcinoma Define Etiologically Distinct Subgroups with Therapeutic Relevance.” Nat. Genet. 48 (10): 1131–41.